Unable to execute about amdock HOT 18 CLOSED

Hi @debanjansen48
You must install the following packages before running it:

 sudo apt install pymol python-qt4 python-numpy openbabel

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I have that before sir.

(base) debanjan@debanjan:~$ sudo apt install python-qt4
[sudo] password for debanjan:
Reading package lists... Done
Building dependency tree
Reading state information... Done
python-qt4 is already the newest version (4.12.1+dfsg-2).
python-qt4 set to manually installed.
The following packages were automatically installed and are no longer required:
avogadro-data cuda-license-10-2 gdal-bin gdal-data grass-doc lib32gcc1
lib32stdc++6 libarmadillo8 libarpack2 libavogadro1 libcharls1
libclang-6.0-dev libclang-common-6.0-dev libclang-dev libdap25
libdapclient6v5 libepsilon1 libfcgi0ldbl libfreexl1 libfyba0 libgdal20
libgdcm2.8 libgeos-3.6.2 libgeos-c1v5 libgeotiff2 libgl2ps1.4 libgtkglext1
libhdf4-0-alt libhdf5-openmpi-100 libjs-jquery-ui libjs-leaflet libkmlbase1
libkmldom1 libkmlengine1 liblas-c3 liblas3 libllvm9 libllvm9:i386
libminizip1 libnetcdf-c++4 libobjc-7-dev libobjc4 libodbc1 libogdi3.2
libopenbabel4v5 libopencv-calib3d3.2 libopencv-contrib3.2 libopencv-core3.2
libopencv-features2d3.2 libopencv-flann3.2 libopencv-highgui3.2
libopencv-imgcodecs3.2 libopencv-imgproc3.2 libopencv-ml3.2
libopencv-objdetect3.2 libopencv-photo3.2 libopencv-shape3.2
libopencv-stitching3.2 libopencv-superres3.2 libopencv-video3.2
libopencv-videoio3.2 libopencv-videostab3.2 libopencv-viz3.2 libpangox-1.0-0
libproj12 libqca2 libqca2-plugins libqgis-analysis2.18.17 libqgis-app2.18.17
libqgis-core2.18.17 libqgis-customwidgets libqgis-gui2.18.17
libqgis-networkanalysis2.18.17 libqgis-server2.18.17 libqgisgrass7-2.18.17
libqgispython2.18.17 libqhull7 libqjson0 libqscintilla2-qt4-13
libqscintilla2-qt4-l10n libqt5positioning5 libqt5qml5 libqt5quick5
libqt5sensors5 libqt5webchannel5 libqt5webkit5 libqwt6abi1 libsocket++1
libspatialindex4v5 libspatialite7 libsuperlu5 libtbb2 liburiparser1
libvtk6.3 libxerces-c3.2 linux-headers-5.3.0-51
linux-headers-5.3.0-51-generic linux-headers-5.3.0-53
linux-headers-5.3.0-53-generic linux-headers-5.3.0-59
linux-headers-5.3.0-59-generic linux-headers-5.3.0-61
linux-headers-5.3.0-61-generic linux-headers-5.4.0-52-generic
linux-headers-5.4.0-53-generic linux-headers-5.4.0-54-generic
linux-headers-5.4.0-56-generic linux-headers-5.4.0-58-generic
linux-headers-5.4.0-59-generic linux-headers-5.4.0-60-generic
linux-headers-5.4.0-62-generic linux-headers-5.4.0-64-generic
linux-headers-5.4.0-65-generic linux-headers-5.4.0-66-generic
linux-headers-5.4.0-67-generic linux-headers-5.4.0-70-generic
linux-headers-5.4.0-71-generic linux-hwe-5.4-headers-5.4.0-52
linux-hwe-5.4-headers-5.4.0-53 linux-hwe-5.4-headers-5.4.0-54
linux-hwe-5.4-headers-5.4.0-56 linux-hwe-5.4-headers-5.4.0-58
linux-hwe-5.4-headers-5.4.0-59 linux-hwe-5.4-headers-5.4.0-60
linux-hwe-5.4-headers-5.4.0-62 linux-hwe-5.4-headers-5.4.0-64
linux-hwe-5.4-headers-5.4.0-65 linux-hwe-5.4-headers-5.4.0-66
linux-hwe-5.4-headers-5.4.0-67 linux-hwe-5.4-headers-5.4.0-70
linux-hwe-5.4-headers-5.4.0-71 linux-image-5.3.0-51-generic
linux-image-5.3.0-53-generic linux-image-5.3.0-59-generic
linux-image-5.3.0-61-generic linux-image-5.3.0-62-generic
linux-image-5.4.0-52-generic linux-image-5.4.0-53-generic
linux-image-5.4.0-54-generic linux-image-5.4.0-56-generic
linux-image-5.4.0-58-generic linux-image-5.4.0-59-generic
linux-image-5.4.0-60-generic linux-image-5.4.0-62-generic
linux-image-5.4.0-64-generic linux-image-5.4.0-65-generic
linux-image-5.4.0-66-generic linux-image-5.4.0-67-generic
linux-image-5.4.0-70-generic linux-image-5.4.0-71-generic
linux-modules-5.3.0-51-generic linux-modules-5.3.0-53-generic
linux-modules-5.3.0-59-generic linux-modules-5.3.0-61-generic
linux-modules-5.3.0-62-generic linux-modules-5.4.0-52-generic
linux-modules-5.4.0-53-generic linux-modules-5.4.0-54-generic
linux-modules-5.4.0-56-generic linux-modules-5.4.0-58-generic
linux-modules-5.4.0-59-generic linux-modules-5.4.0-60-generic
linux-modules-5.4.0-62-generic linux-modules-5.4.0-64-generic
linux-modules-5.4.0-65-generic linux-modules-5.4.0-66-generic
linux-modules-5.4.0-67-generic linux-modules-5.4.0-70-generic
linux-modules-5.4.0-71-generic linux-modules-extra-5.3.0-51-generic
linux-modules-extra-5.3.0-53-generic linux-modules-extra-5.3.0-59-generic
linux-modules-extra-5.3.0-61-generic linux-modules-extra-5.3.0-62-generic
linux-modules-extra-5.4.0-52-generic linux-modules-extra-5.4.0-53-generic
linux-modules-extra-5.4.0-54-generic linux-modules-extra-5.4.0-56-generic
linux-modules-extra-5.4.0-58-generic linux-modules-extra-5.4.0-59-generic
linux-modules-extra-5.4.0-60-generic linux-modules-extra-5.4.0-62-generic
linux-modules-extra-5.4.0-64-generic linux-modules-extra-5.4.0-65-generic
linux-modules-extra-5.4.0-66-generic linux-modules-extra-5.4.0-67-generic
linux-modules-extra-5.4.0-70-generic linux-modules-extra-5.4.0-71-generic
proj-data python-appdirs python-backports.functools-lru-cache python-certifi
python-colorama python-cycler python-dateutil python-decorator
python-easydev python-jinja2 python-markupsafe python-matplotlib-data
python-owslib python-pexpect python-psycopg2 python-ptyprocess
python-pyparsing python-pyproj python-pyspatialite python-qscintilla2
python-qt4-sql python-requests python-subprocess32 python-tz python-yaml
qgis-common qgis-plugin-grass-common qgis-providers qgis-providers-common
qml-module-qtgraphicaleffects qml-module-qtquick-controls
qml-module-qtquick-dialogs qml-module-qtquick-layouts
qml-module-qtquick-privatewidgets qml-module-qtquick-window2
qml-module-qtquick2 qt4-designer xsane-common
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 81 not upgraded.

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same issue...

from amdock.

What Linux distribution are you using?
Is python2 the default python in the terminal?

Run this and show me the output
python
import PyQt4

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Linux Mint 19.3 Cinnamon version 4.4.8

Linux kernal : 5.4.0-73-generic

(base) debanjan@debanjan:~$ python
Python 3.8.2 (default, Mar 26 2020, 15:53:00)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

import PyQt4
Traceback (most recent call last):
File "", line 1, in
ModuleNotFoundError: No module named 'PyQt4'

(base) debanjan@debanjan:~$ whereis python
python: /usr/bin/python3.6 /usr/bin/python3.6m /usr/bin/python /usr/bin/python3.6m-config /usr/bin/python3.6-config /usr/bin/python3.8 /usr/bin/python2.7-config /usr/bin/python2.7 /usr/lib/python3.6 /usr/lib/python3.8 /usr/lib/python3.7 /usr/lib/python2.7 /etc/python3.6 /etc/python /etc/python3.8 /etc/python2.7 /usr/local/lib/python3.6 /usr/local/lib/python3.8 /usr/local/lib/python2.7 /usr/include/python3.6 /usr/include/python3.6m /usr/include/python2.7 /usr/share/python /home/debanjan/miniconda3/bin/python3.8-config /home/debanjan/miniconda3/bin/python /home/debanjan/miniconda3/bin/python3.8 /usr/share/man/man1/python.1.gz

from amdock.

Ok, the error is because you have a conda environment active.
AMDock works with the system python and only with version 2. We are working on the new version with python3 since python 2 is obsolete. You can modify the AMDock.sh file in the installation folder to explicitly specify the system python2 or deactivate the conda environment

Python executable in AMDock.sh

# ---------------------------------------------------------------------# 
Locate a python2.7 installation directory which will be used to run the program.
# ---------------------------------------------------------------------
PYTHON="python"

change it by

PYTHON="/usr/bin/python2"

from amdock.

Hureee
thank you....Its working....

Thanks a lot.

One silly thing I would like to ask you if u don't mistake me...shall I convert protein.pdb file into protein.pdbqt file using this program?

from amdock.

Not necessarily, AMDock supports both the PDB file to generate the PDBQT and a PDBQT file. Typically, users enter a PDB since AMDock carries out the protonation and preparation. However, if necessary you can use the PDBQT prepared in ADT or Openbabel

from amdock.

why I am receiving this error "Prepare_gpf4zn finalized with exitcode 1 and existstatus 0"

can dock set of ligands or a batch or ligands with this tool??

the error is

Traceback (most recent call last):
File "/home/debanjan/AMDock-master/AMDock/AMDock/programs/prepare_gpf4zn.py", line 134, in
key,newvalue = string.split(p, '=')
ValueError: need more than 1 value to unpack

from amdock.

It could be a bug, I will check it as soon as possible.

Unfortunately no, currently AMDock does not support virtual screening. However, you can prepare the receptor with AMDock and then each ligand with a script. The receptor's pdbqt file can be found in the input folder inside of project folder

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ok, thank you.

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another error
PDB2PQR finalized with exitcode 2 and existstatus 0

the log given below

Welcome to AMDock
Version 1.5.2 For Windows and Linux

AMDOCK: Defining Initial Parameters...
AMDOCK: DOCKING_PROGRAM: AutoDock Vina
AMDOCK: WDIR: /home/debanjan/Documents/ssp/AMDock/tst-vina
AMDOCK: MODE: SCORING
AMDOCK: TARGET: 4qu3-prep
AMDOCK: TARGET (Hetero): []
AMDOCK: TARGET (Zn atoms): []
AMDOCK: LIGAND: 4qu3-lig
AMDOCK: LIGAND (heavy_atoms): 33
AMDOCK: Defining Initial Parameters... Done
AMDOCK: Prepare Initial Files...
AMDOCK: Running PDB2PQR for Target...

Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH

pdb2pqr.py: error: Unable to find file /home/debanjan/Documents/ssp/AMDock/tst-vina/input/4qu3-prep.pdb!

PDB2PQR - a Python-based structural conversion utility

Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).

AMDOCK: MODE: SCORING
AMDOCK: TARGET: 4qu3-prep
AMDOCK: TARGET (Hetero): []
AMDOCK: TARGET (Zn atoms): []
AMDOCK: LIGAND: 4qu3-lig
AMDOCK: LIGAND (heavy_atoms): 33
AMDOCK: Defining Initial Parameters... Done
AMDOCK: Prepare Initial Files...
AMDOCK: Running PDB2PQR for Target...

Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH

pdb2pqr.py: error: Unable to find file /home/debanjan/Documents/ssp/AMDock/tst-vina/input/4qu3-prep.pdb!

During AutoDock 4.2 exercise encountered by similar error

AMDOCK: Defining Initial Parameters...
AMDOCK: DOCKING_PROGRAM: AutoDock4
AMDOCK: WDIR: /home/debanjan/Documents/ssp/AMDock/tst_adt
AMDOCK: PARAMETERS_FILE: AD4_parameters.dat
AMDOCK: MODE: SIMPLE
AMDOCK: TARGET: 4qu3-prep
AMDOCK: TARGET (Hetero): []
AMDOCK: TARGET (Zn atoms): []
AMDOCK: LIGAND: 4qu3-lig
AMDOCK: LIGAND (heavy_atoms): 33
AMDOCK: Defining Initial Parameters... Done
AMDOCK: Prepare Initial Files...
AMDOCK: Running PDB2PQR for Target...

Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH

pdb2pqr.py: error: Unable to find file /home/debanjan/Documents/ssp/AMDock/tst_adt/input/4qu3-prep.pdb!

PDB2PQR - a Python-based structural conversion utility

Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).

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I have similar problems. First of all, I cannot run ./install.sh. I get the following error:

Traceback (most recent call last): File "/home/aroy/Applications/AMDock-master/module_checker.py", line 24, in <module> obmayor, obminor, obrel = obabel_exe.communicate()[0].split()[2].split('.') TypeError: a bytes-like object is required, not 'str'

Moreover, I pip is constantly complaining that Python2.7 is no longer supported. Are there any plans to upgrade the version of Python?

I am using Fedora 34, with all the latest packages installed.

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Hi @debanjansen48. Sorry for the delay.

My PhD commitments keep me running a marathon and really, I completely forgot about the report.

I can't reproduce the error. I thought it was the file name that has the "-" character. However, it seems to work well for me. Can you try removing or changing these characters to "_" ​from the file names?

Can you tell me if the files are in that directory? It could happen that the directory is not changed or the file cannot be copied to the input folder, which should show an error.
You can also run AMDock in a console, which will display the debugging data. Just run the AMDock.sh file found inside the installation directory. You send me this information, I promise to take care of the error as soon as possible

from amdock.

Hi @Shredderroy. Thanks for report this error.
Can you tell me what version of python you are using?
This error seems to be related to the python that is by default in the PATH.
Make sure the python executable that install.sh is using is the python2 executable. It currently uses the system python, so it is probably Python3 since modern OS already uses it by default.

Unfortunately, this version only works with Python2. We are working on the version with Python3. However, since the design of the program was not good (difficult to maintain, update or implement new functions) we decided to improve it. This will delay a bit longer than expected, but I think it will be worth it. Another and more important thing, AMDock2 is not funded by any project, but what time we can dedicate to it are the hours of rest. Already the doctorate is a considerable work, I also have two students to advise and my thesis project. We are making a huge effort to launch AMDock2, so we ask our users for a little patience. We are very excited to launch it as according to our ambition and prospects, it will be great.

Best!
Mario S.

from amdock.

Hi @Valdes-Tresanco-MS,

Thank you very much for such a prompt response. I fully understand your commitments, and I wish you the best with your studies.

I created a new virtualenv called amdock-env in Fedora 34, in which I installed Python 2.7. So, when I activate this virtual environment and type python at the prompt, I get Python 2.7.

I would like to add that the Windows 10 version seems to run without any error.

Thanks again for your work in making this tool available to us at no cost!

Best wishes,

A. R.

from amdock.

Halloo @Valdes-Tresanco-MS I will work on it and let you inform. Just received your advice. I am sorry, I need to take some classes now. After that, post evening I will go to my system and let you know. Thanks for your response.

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yes. That was working nicely. Thank you.

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